DATA ANALYSIS 

HIMSR resources for analyses of the immune response 

HIMSR will help you cover all of your analysis needs by offering self-service and fee-for-service access to state-of-the-art analysis software.

inForm
inForm is an automated image analysis software package that uses trainable algorithms in a user-friendly interface to accurately visualize and quantify biomarkers in tissue sections from the Vectra 3.0 and Vectra Polaris. Capability includes phenotyping, co-localization, co-expression, tissue region detection (e.g. tumor versus stroma), nearest-neighbor quantification, and traditional scoring functions. Cell type identification and localization allows downstream analyses including density of each cell type within each tissue, quantification of cell-cell contacts, and distances between cell types and tissue types. This software is available for use on a dedicated analysis station within the HIMSR (sign up for time on the iLab calendar) or, for larger projects, check out a copy of inform from the HIMSR ($). We offer periodic workshops to help you get started with inForm and Phenoptr Reports and Akoya Biosciences’ also have great new videos on how to use these softwares [inForm and Phenoptr Reports.

FlowJo

The FlowJo™ workspace is used for a variety of cytometry quantification analyses, including immunophenotyping, cell cycle, proliferation, kinetics studies, quantitative population comparison, and plate screening assays. This software is available through the Cancer Center Flow Cytometry Core.

MIBItracker Software  (scroll to bottom of webpage)
MIBItracker is a cloud-based software that lets you easily review slide and image data. It is easily accessible through a web browser. You can customize the display for each image or image set including selecting channels for overlay, setting channel relative intensity, pixel smoothing, and channel pseudo-color.

Additional Resources
Bioinformatics Core https://medschool.cuanschutz.edu/bioinformaticscore

Center for Innovative Design and Analysis https://www.ucdenver.edu/academics/colleges/PublicHealth/research/centers/cbc/Pages/welcome.aspx

Biostatistics & Bioinformatics Shared Resource
https://medschool.cuanschutz.edu/colorado-cancer-center/research/shared-resources/biostatistics-shared-resource